Not completely sure but I would like to say "command" can be a process/binary for a system but "instructions" are at the lowest level of communication. "Instruction" word is used at processor level such as 8080 microprocessor while "command" term is used at user space such as linux command "ls" "cd" etc.
Command is at high level while instruction is used for the lowest level in a computer system. When we issue a command such as "ls" finally it becomes instructions for processors.
